The SWAT model developed by the USDA-Agricultural Research service for the prediction of rainfall runoff, sediment, and chemical yields in a basin was applied to Jeju Island watershed to estimate the amount of runoff. The research outcomes revealed that the estimated amount of runoff for the long term on 2 watersheds showed fairly good performance by the long-term daily runoff simulation. The watershed of Chunmi river located the eastern region in Jeju Island, after calibrations of direct runoff data of 2 surveys, showed the similar values to the existing watershed average runoff rate as 22% of average direct runoff rate for the applied period. The watershed of Oaedo river located the northern region showed R2 of 0.93, RMSE of 14.92 and ME of 0.70 as the result of calibrations by runoff data in the occurrence of 7 rainfalls.